I have witnessed a change in the Hampton additive screen some years ago - on
purpose - the formulation simply did not work OK. So I guess there are
changes occasionally.
Jan
On Wed, Aug 24, 2011 at 5:21 PM, Chris Morris wrote:
> HI,
>
> I've recently seen two examples where the description of a
Hi Yuri,
a possible option:
phenix.model_vs_data model.pdb data.mtz will do it. Look for lines like this
in the output:
ADP (min,max,mean):
all (136 atoms): 4.497.6 25.3
side chains (48 atoms): 4.996.8 21.0
main chains (64 atoms): 4.497
Quick newbie question,
After i get my output file from baverage containing the average b-factor and
rms by residues,
How can I calculate and display the average (and or mean) B-factors?
Is there a way of calculating it by protein, ligands and solvent separately?
thank you
Thanks, David. I believe the leaked column was probably my case,
although I didn't see any visible leakage I re-tightened connections
anyway. But the weird thing was that after I equilibrized the column
for a while, the dry patches and cracks disappeared. Everything
returned to normal even a standa
I'm glad this worked out well for you. For
conducting molecular sizing determinations with a calibrated GEC
column, I typically use 100-500 uL injections of approximately 1
mg/mL or so of purified protein on a 1.6 x 60 cm column. The
limited protein quantity will
Hello
Space groups with point groups 622 and 432 merohedral twinning is not possible
(they are the highest groups possible for proteins).
If you could merge in 622 it means that Rmerge was very small. It is very
likely that point group is either 622 or 6 with very strong rotational symmetry
th
Hello All,
This is regarding twinning in a data set.
I collected a native data set to resolution, 1.8 A. I used XDS suite
to process and scale the data set. It scaled well in P622 and I found
systematic absence (l=6n present).
Hence thought the space group may be P6122/P6522. SFCHECK did not
Thanks everyone for your response.
The most likely answer to my problem is protein overloaded onto the
column. I pushed my protein concentration further down to 0.5ml
instead of the usual method, which to run multiple times on SEC.
Adding NaCl in the buffer may also help, as it seems that t
To add to what Pat has mentioned, I work with a protein that has a number of
exposed Cys residues, and it turns into a gel at 4 degrees within a week, even
if I store it in buffer with reducing agents. This happens every time I store
it at 4 degrees. To test if your "jelly" is due to S-S crossli
I had a similar problem with crystals that were obtained from PEG-based
precipitants over long periods of time. If I harvested the crystals in
about 5 days, they would diffract to ~3 Angstrom. If I let them grow any
time past about 7 days, they became PEG-alated and didn't diffract at
all. I person
Personally, I like having the GUI front end for
training and education, especially for undergraduates. It has made
protein XRD much more accessible as a tool for many labs that
would otherwise find the barrier for entry very high. In the "old
days,"--8 years ago (
Certainly not unprecedented, or even that unusual (I remember making gels from
BSA and IgG solutions during grad school rotations). Gel formation usually
requires crosslinking, so consider whether you might be getting adventitious
disulfide bond formation.
Pat
On 30 Aug 2011, at 11:31 AM, aido
Not necessarily uncommon. To minimize
protein-protein interactions that might be causing gelation, you
might change the pH of the solution so that is is not close to the
pI, use a small amount of chelator to sequester metal ions, and
maintain a modest ionic streng
On 08/26/2011 10:18 AM, REX PALMER wrote:
Once waters have been located and refined is there a program that analyses
their positions
in terms of solvation shells?
Can the results be compared easily with those from related known
protein structures?
Rex Palmer
http://www.bbk.ac.uk/biology/our-sta
I have had protein crystals (so very high protein concentration) that turn
into gummy bear-like objects, where instead of crumbling they are like,
well, a gummy bear or a piece of rubber. I attributed it to oxidation or
other chemical ageing processes. I am sure others will have suggestions for
p
Dear Buddies,
Sorry for bothering you with an off-ccp4 question. We recently are
experiencing a very strange phenomena. A couple of protein preps with
reasonably high concentration (10-20mg/ml) become a jelly after
storages for overnight or a couple of days at 4C. All of them have
been
On Tue, 2011-08-30 at 09:55 -0500, Pete Meyer wrote:
> but I'm all in favor of dropping gui's for tasks
> that don't involve dealing with graphical data
second that. I was about to say "while it is not expected that everyone
practicing crystallography should master the use of command line", but
Paul Smith wrote:
2) ditch all gui support or, from scratch, develop a gui front-end that uses
none of the following: Qt, Ruby, Perl, Python, TK/TCl, etc. This gui must
compile and run on all mainstream hardware on all major operating systems. The
custom gui might also need a custom driver
Hi Eswar
Firstly, I would certainly try crystal seeding into random screens if
you haven't already tried it. Refs below.
Secondly, it's very convenient to grow the crystals under oil, and to
soak the organic solvents into the drops, through the oil. This makes
it much easier to harvest the crys
Hi Andrea,
If you haven't already done so it might be worth trying a room temperature
mount (capillary or in-situ) to get a feeling for how well the crystals
diffract to start with.
Dave
David Hargreaves
Associate Principal Scientist
There are some windows only software, for example 3ds Max. But you have a
point, you probably don't need linux system in this case.
Nian
On Tue, Aug 30, 2011 at 1:55 AM, Antony Oliver
wrote:
> Erm, somewhat confused — if you are going to buy a Mac — why would you
> need (or want!) a triple boo
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